5WTQ | pdb_00005wtq

Crystal structure of human proteasome-assembling chaperone PAC4

• PDB DOI: https://doi.org/10.2210/pdb5WTQ/pdb

• Classification: CHAPERONE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-12-13 Released: 2017-03-22 
• Deposition Author(s): Kurimoto, E., Satoh, T., Ito, Y., Ishihara, E., Tanaka, K., Kato, K.
• Funding Organization(s): JSPS KAKENHI

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.254 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Literature

Crystal structure of human proteasome assembly chaperone PAC4 involved in proteasome formation

Kurimoto, E., Satoh, T., Ito, Y., Ishihara, E., Okamoto, K., Yagi-Utsumi, M., Tanaka, K., Kato, K.

(2017) Protein Sci 26: 1080-1085

• PubMed: 28263418 
• DOI: https://doi.org/10.1002/pro.3153
• Primary Citation Related Structures: 
  5WTQ


• PubMed Abstract: 
  

  The 26S proteasome is a large protein complex, responsible for degradation of ubiquinated proteins in eukaryotic cells. Eukaryotic proteasome formation is a highly ordered process that is assisted by several assembly chaperones. The assembly of its catalytic 20S core particle depends on at least five proteasome-specific chaperones, i.e., proteasome-assembling chaperons 1-4 (PAC1-4) and proteasome maturation protein (POMP). The orthologues of yeast assembly chaperones have been structurally characterized, whereas most mammalian assembly chaperones are not. In the present study, we determined a crystal structure of human PAC4 at 1.90-Å resolution. Our crystallographic data identify a hydrophobic surface that is surrounded by charged residues. The hydrophobic surface is complementary to that of its binding partner, PAC3. The surface also exhibits charge complementarity with the proteasomal α4-5 subunits. This will provide insights into human proteasome-assembling chaperones as potential anticancer drug targets.

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Organizational Affiliation: 
• Faculty of Pharmacy, Meijo University, Tempaku-ku, Nagoya, 468-8503, Japan.
Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, 467-8603, Japan.
JST, PRESTO, Mizuho-ku, Nagoya, 467-8603, Japan.
Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, 156-8506, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.6 kDa 
• Atom Count: 3,763 
• Modeled Residue Count: 433 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome assembly chaperone 4	A, B, C, D	126	Homo sapiens	Mutation(s): 1  Gene Names: PSMG4, C6orf86, PAC4
UniProt & NIH Common Fund Data Resources
Find proteins for Q5JS54 (Homo sapiens) Explore Q5JS54  Go to UniProtKB:  Q5JS54
PHAROS:  Q5JS54 GTEx:  ENSG00000180822

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	E [auth A], G [auth B], J [auth C], L [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	F [auth A], H [auth B], I [auth B], K [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.254 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.548	α = 90
b = 152.779	β = 90
c = 212.911	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-03-22 
Deposition Author(s): Kurimoto, E., Satoh, T., Ito, Y., Ishihara, E., Tanaka, K., Kato, K.

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Funding Organization	Location	Grant Number
JSPS KAKENHI	Japan	15H02491, 25102008

Revision History  

• Version 1.0: 2017-03-22
  Type: Initial release
  
• Version 1.1: 2017-05-24
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations, Refinement description